What I want to do is identify column 1 of FILE1 with the ># on FILE2. So for example, 1154 from FILE1 will match up with 1154 from FILE2. Next, I want it to identify the value on column 2 (so for 1154, it will identify the 10th letter which happens to be G). So if column 3 of FILE1 is + then it will print the first 8 letters in from of it (i.e. the 8 letters in front of G would be TCTCACTC). But if is it – on column 3, then it will take the reverse. So for ABF2 on “584” it will take the top 8 sequences starting from the reverse end. So instead of starting at “G” at >584, it will start at “T” (the end). So the position of ABF2 will be 25 letters away from “T” , so the letter will be “C”. Then it will take the values behind it… so CCACTTCC.

The output file will print out column 4 of FILE1, the top 8 letters from FILE2 and column 3 from FILE1.

The final file (FILE3) will look like this:

AAD6 TCTCACTC + ABF2 CCACTTCC -

Could someone give me some help on this! I am new to perl and I am put in a situation where I have to program at a very high level.

Re: [kylle345] Need a program that prints out letters from another file
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Dear friend It can be done but you are not clear in your requirement. Always use "Preview Post" button before posting. The forward strand requirement is clear I guess you want to design some primers for PCR amplification or some similar experiment. But the reverse strand requirement is not clear "So----“584” so---- “G” so---- “T” so--- “T” so--- “C”- so-… " So dear friend what is "“T”". If the end base pair is taken as starting point then in case of "584 10 - ABF2" you should be looking for "ACTTCCCC" (if the last thymine is to be taken as "start/ 0-point") but how you are counting "CCACTTCC" is not clear. -For all my suggestions " I am sure someone else can do it in a better or elegant manner!"